crossing96/oncoscreening huggingface dataset:
Harnessing Nature: Computational and Experimental Insights Into Ipomoea obscura Metabolites for Bladder Cancer Therapy.	Ipomoea obscura (L.), a medicinal plant from the Convolvulaceae family, has been traditionally used to treat various ailments. This study evaluated the in vitro cytotoxicity of its ethanolic leaf extract against human bladder cancer T24 cells and investigated its phytochemical constituents through computational methods. The extract exhibited dose-dependent cytotoxicity with an IC(50) of 82.10 µg/mL, comparable to doxorubicin (75.04 µg/mL). Among 35 screened phytocompounds, kaempferol, oleic acid, and ursodeoxycholic acid showed strong binding affinity toward carbonic anhydrase IX (CA IX), with Glide docking scores ranging from -8.86 to -6.96 kcal/mol. These compounds formed stable Zn(2+) coordination and hydrogen-bonding interactions within the CA IX active site. Molecular dynamics simulations confirmed the stability of the ligand-protein complexes, and MM/GBSA analysis revealed favourable binding free energies. These findings indicate that the ethanolic leaf extract of I. obscura possesses anticancer activity against bladder cancer cells, potentially mediated through CA IX inhibition. Kaempferol, oleic acid, and ursodeoxycholic acid are likely contributors and warrant further investigation for their therapeutic potential in cancer treatment.	bladder
The CD8(+)/Foxp3(+) ratio, but not the number of OX40(+) TILs, is an independent predictor of tumor recurrence in non-muscle-invasive bladder cancer: a retrospective study.	Non-muscle-invasive bladder cancer (NMIBC) frequently recurs and progresses into an aggressive and lethal entity within five years. The clinical management of recurrent tumors remains limited. Therefore, identifying individual patients who are at a high risk of recurrence is crucial for early clinical monitoring and appropriate medical intervention, which may lead to improved outcomes. OX40 is a dual modulator that stimulates effector T cells and suppresses Tregs. It appears to be an ideal molecule for predicting survival outcomes, surpassing the predictive power of single or combined T cell signatures. It has been shown to act as an independent tumor prognostic predictor in various cancers, including non-small cell lung cancer, melanoma, and colorectal cancer. However, its potential as a prognostic tool for tumor recurrence in NMIBC has yet to be investigated. The present study aimed to investigate the potential value of OX40 as a predictor of recurrence risk in patients with NMIBC. Additionally, its downstream effectors, Foxp3 and CD8, were also evaluated. Tissue samples were collected from a cohort of 110 patients diagnosed with NMIBC. Immunohistochemistry was performed to assess the density of stromal OX40(+), Foxp3(+), and CD8(+) tumor infiltrating lymphocytes (TILs). Following survival analysis using the Kaplan-Meier method and log-rank test, we found that tumor recurrence was associated with a decreased density of OX40(+) and CD8(+) TILs, an elevated density of Foxp3(+) TILs, and lower ratios of OX40(+)/Foxp3(+) and CD8(+)/Foxp3(+) TILs. However, after adjustment, multivariate COX regression analysis indicated that only the ratio of CD8(+)/Foxp3(+) was an independent predictor of recurrence risk. The prediction power was assessed by a receiver operating characteristic (ROC) curve analysis. The results demonstrated that the AUC value for the CD8(+)/Foxp3(+) ratio was better than the other predictive markers. Although the expression of OX40 in TILs was associated with tumor recurrence, our results suggest that the predictive efficacy of a combination of CD8 and Foxp3 was more robust after adjustment. Future research utilizing advanced immunotyping techniques is necessary to validate these findings in larger cohorts.	bladder
Comparative Analysis of CT and MRI Combined with RNA Sequencing for Radiogenomic Staging of Bladder Cancer.	Accurate staging of bladder cancer (BCa) is important for identifying optimal treatment. Currently, clinical tumor staging for BCa relies on computed tomography (CT) scans, but these can lead to under- or overstaging of patients. Recent research suggests that using magnetic resonance imaging (MRI) along with RNA sequencing (RNASeq) gene expression analysis can provide more precise staging. In this study, 31 matched CT scans, MRI images, and formalin-fixed, paraffin-embedded (FFPE) tissues were collected. First, two radiologists reviewed the images for staging BCa. Next, radiomics features were extracted from both CT and MR images, and computational radiogenomics analyses were performed. Subsequently, RNASeq was performed using FFPE tissues of TURBT prior to cystectomy. A radiogenomic analysis was conducted to identify advanced T-stage signatures. Regarding imaging alone, MRI was found to be more accurate in staging >T2 compared to CT scans. Within a retrospective cohort, MRI radiogenomic signatures were more effective in staging patients than CT, with genomic features playing a significant role. Using canonical correlation analysis, we additionally identified radiomic features underlying genomic signatures of advanced tumor stage. When applying these signatures across a small prospective cohort, MRI radiomic data were able to stratify stage; however, the addition of the same genomic features did not improve the sensitivity and specificity of the model. These preliminary results are promising, but additional research with larger sample sizes is needed to draw definitive conclusions and explore further correlations and statistical interactions between genes and imaging features through machine learning techniques as we move radiogenomics to the clinic.	bladder
Robotic Partial Cystectomy for Urachal Adenocarcinoma: Surgical Technique with Cys-toscopic Correlation.	INTRODUCTION AND OBJECTIVE: Urachal adenocarcinoma is a rare malignancy that typically arises from the bladder dome and is often diagnosed incidentally or during evaluation for hematuria (1, 2). Surgical excision remains the cornerstone of treatment (3, 4). This video demonstrates the robotic technique for partial cystectomy with en bloc urachal resection, combined with synchronized intraoperative cystoscopic imaging-an approach that has proven feasible and oncologically safe in selected cases (5-7). MATERIALS AND METHODS: A 74-year-old hypertensive male presented with self-limited gross hematuria. Cystoscopy revealed a lesion at the bladder dome, and transurethral resection confirmed urachal adenocarcinoma. Staging chest and abdominal CT scans showed no evidence of metastasis. Robotic partial cystectomy with urachal excision was performed using a da Vinci platform and an auxiliary 5-mm port, in line with contemporary minimally invasive techniques, including single-port surgery (8). The urachus was dissected to the umbilicus, the bladder dome excised, and the bladder closed in two layers with barbed sutures. The specimen was retrieved through the umbilical incision following concomitant umbilectomy. Intraoperative cystoscopy provided simultaneous tumor visualization via picture-in-picture overlay. RESULTS: Operative time was 45 minutes, with an estimated blood loss of 20 mL and no complications. The patient was discharged on postoperative day one with a Foley catheter, which was removed after seven days. Pathological analysis revealed moderately differentiated urachal adenocarcinoma with a mucinous component, detrusor and perineural invasion, and negative margins. At 6-month follow-up, the patient remained asymptomatic, continent, and recurrence-free on surveillance CT. CONCLUSION: Robotic partial cystectomy with urachal excision is a safe and effective treatment for localized urachal adenocarcinoma. Intraoperative cystoscopy enhances anatomical correlation and may contribute to oncologic safety.	bladder
CT-based Radiomics of Intratumoral and Peritumoral Regions to Predict the Recurrence Risk in Patients with Non-muscle-invasive Bladder Cancer within Two Years after TURBT.	BACKGROUND: Predicting the recurrence risk of NMIBC after TURBT is crucial for individualized clinical treatment. OBJECTIVE: The objective of this study is to evaluate the ability of radiomic feature analysis of intratumoral and peritumoral regions based on computed tomography (CT) imaging to predict recurrence in non-muscle-invasive bladder cancer (NMIBC) patients who underwent transurethral resection of bladder tumor (TURBT). METHODS: A total of 233 patients with NMIBC who underwent TURBT were retrospectively analyzed. Within the intratumoral and peritumoral regions of the venous phase images, 1316 radiomics features were extracted. Feature selection was used to identify a set of top recurrence-associated features within the training cohort. Three models were constructed to predict recurrence for a given patient using Random Forest (RF): Model 1 was based on the radiomics features set from the intratumoral region, Model 2 was based on a combination of intratumoral and peritumoral regions, and Model 3 combined the radiomics features from Model 2 and clinical factors. The three models were then independently tested on internal and external cohorts, and their performance was evaluated. We also employed the bootstrap method on the internal cohort to further validate the performance of the model. RESULTS: Combining intratumoral and peritumoral regions, Model 2 yielded a higher area under the receiver operator characteristic curves (AUC) than Model 1, with 0.826 AUCs of the training cohort. After adding clinical factors, the predictive performance of Model 3 for postoperative recurrence of NMIBC was further improved, and the AUCs of the training, internal, and external validation cohorts of Model 3 were 0.860 (95% CI: 0.829-0.954), 0.829 (0.812-0.863), and 0.805 (0.652-0.840), respectively (all p>0.05). The bootstrap value of Model 3 on the internal cohort was 0.852. Model 3 stratified patients into high- and low-risk groups with significantly different recurrence-free survival (RFS) (p<0.001). CONCLUSION: Radiomic features derived from intratumoral regions can predict the 2-year recurrence risk following TURBT in patients with NMIBC. The predictive performance is further enhanced when combined with radiomic features from peritumoral regions and clinical risk factors.	bladder
Association between symptoms of acute cystitis and findings of bladder cancer in the Swedish standardized pathway for macroscopic haematuria.	Standardized Care Pathway (SCP) for patients presenting with macroscopic haematuria was introduced in Sweden in 2015. In contrast to neighbouring countries, the Swedish model includes all patients with macroscopic haematuria above the age of 50, notwithstanding obvious causes. The aim of this study was to characterize the patients referred within the SCP and the presence of acute cystitis. All patients admitted to two regional hospitals in 2023, under the terms of SCP macroscopic haematuria, were included. Patient data were collected retrospectively regarding age, sex, symptoms of cystitis and cause of haematuria. The study included 782 patients. The median age was 70 years and half were women. In 89 cases, a urinary tract cancer was found (11%) and 74 (9%) had bladder cancer. The cancer-positive group was significantly older (median 75 years) and 76% were men. Half of patients (51%) had symptoms of acute cystitis on referral. This was significantly associated with the absence of bladder cancer, but only in the age groups 50-69, where no case was found among patients with symptoms of cystitis. In the age groups above, 22 cancer-positive patients (30% of all bladder cancer cases) had symptoms of cystitis. The Swedish SCP macroscopic haematuria targets younger female patients unproportionally, in comparison to where cancer is likely found. Neither symptoms of cystitis, nor positive urine cultures exclude bladder cancer in elderly, but clearly in the age groups 50-69. If excluding the latter from the SCP, a 28% reduction of examined patients can be achieved with a negligible risk of missing cancer.	bladder
Impact of COVID-19 care reorganization on the prognosis of patients with bladder urothelial carcinoma: a multicentric retrospective study.	BACKGROUND: The COVID-19 pandemic disrupted healthcare systems globally, raising concerns about delayed cancer diagnosis and treatment. In France, transurethral resection of bladder tumors (TURBT) was prioritized in national urology guidelines to ensure the timely management of urothelial carcinoma. This study aimed to assess the impact of care reorganization on tumor staging, recurrence, palliative care, and mortality in bladder cancer patients from the pre-pandemic through late-pandemic periods. METHODS: We conducted a retrospective multicenter study including all patients who underwent TURBT with histologically confirmed urothelial carcinoma between April and December of 2019 (pre-pandemic), 2020 (early pandemic), 2021 (mid-pandemic), and 2022 (late pandemic) in two French institutions. TURBT indications were categorized as diagnostic, palliative, or staging. Clinical and pathological data were compared across the four periods. Statistical analyses included Chi-square tests, Estimated Annual Percentage Change (EAPC), and multivariable logistic regression adjusted for age, sex, ASA score, and center. RESULTS: A total of 790 TURBT procedures were analyzed. The proportion of muscle-invasive bladder cancer (pT ≥ 2) declined over time (18.7% in 2019 to 13.2% in 2022; p = 0.63), while superficial tumors (pTa) increased (57.2% to 65.5%). All-cause mortality significantly decreased from 38.0% in 2019 to 22.0% in 2020, 20.5% in 2021, and 19.5% in 2022 (p = 0.006). EAPC showed a significant annual decline in mortality (-24.3%, p = 0.004). In multivariable analysis, 2020, 2021, and 2022 were each associated with significantly lower odds of mortality compared to 2019. Recurrence rates remained stable across all periods (p = 0.93). Inter-hospital variation persisted in mortality and recurrence. CONCLUSIONS: Despite the pandemic, urothelial bladder cancer outcomes did not worsen through 2022. On the contrary, timely reorganization, prioritization of TURBT, and triage strategies were associated with reduced mortality and palliative care needs, highlighting the resilience of cancer care when guided by adaptive health policies.	bladder
Prognostic value of prostate volume and nomograms for predicting recurrence in patients with non-muscle invasive bladder cancer: a multi-institutional study.	PURPOSE: We conducted an assessment to investigate the impact of prostate volume on the recurrence of patients with non-muscle invasive bladder cancer (NMIBC). Subsequently, we developed and validated nomograms to accurately evaluate recurrence in NMIBC patients. Additionally, we examined the potential improvement in predictive capability achieved by introducing prostate volume as a variable in the model. METHODS: We conducted a retrospective analysis, enrolling 555 eligible patients from seven independent medical institutions across China. We first evaluate recurrence-free survival outcomes in patients with varying prostate volumes. Subsequently, we divided patients into a training cohort and an external validation cohort. Univariate and multivariate Cox regression analyses were conducted within the training cohort. Accordingly, two nomogram models with and without prostate volumes were developed. Their performance was compared by concordance index, calibration curves, receiver operating characteristics curves, and decision curve analysis. Furthermore, a risk classification model utilizing the nomogram incorporating prostate volume was developed. RESULTS: The 3-year recurrence-free survival was markedly lower in patients with large prostate volumes (> 30 ml) compared to those with relatively small prostate volumes (< 30 ml) (p < 0.001). The AUC for the model incorporating prostate volume at 3 years in the training cohort and external validation cohort was 0.828 and 0.811, surpassing the AUC for the model excluding prostate volume at the corresponding intervals, which was 0.796 and 0.778. The 1- and 2-year AUC for the two models also exhibited similar differences. The decision curve analysis results demonstrated the significant superiority of the nomogram incorporating prostate volume over the one without it. CONCLUSION: Our investigation revealed that prostate volume significantly influences recurrence in patients with NMIBC. We successfully developed a more accurate nomogram by introducing prostate volume as a variable and provided new insights to further guide clinical management and individualized treatment of NMIBC patients.	bladder
Phenolic zingerone nanoparticles impede cell cycle progression to compete against human urothelial carcinoma.	Civilization diseases including cancer are caused by more than 80 % of worldwide lethal. Phytochemicals-based methodologies for cancer chemoprevention, adjuvant chemotherapy, and anti-carcinogenic progression have caught the attention of modern medicines and become one of the explicit trends for cancer prevention and therapeutic strategies. In this study, we fabricated the phytochemical-derived zingerone nanoparticles (NPs) and examined their effects on anti-tumorigenicity and the related signaling mechanisms in two human urothelial carcinoma (UC) BFTC905 and BFTC909 cell lines. Our results demonstrated that zingerone NPs significantly elicited cytotoxicity and inhibited in vitro tumorigenesis in these human UC cells. Moreover, zingerone NPs impeded cell cycle progression and induced cell apoptosis in a dose-dependent manner. TUNNEL assay further supported that zingerone NPs markedly triggered cell apoptosis. Molecular mechanisms analysis further demonstrated that zingerone NPs dramatically interfered with CDKs and Cyclins involved in cell cycle progression including inhibition of CDK6, CDK4 and Cyclin D1, CDK2 and Cyclin A2, and CDK1 and Cyclin B1, in the G1, S, and G2/M phases respectively. Interestingly, TCGA database analysis also indicated that upregulation of cell cycle transition factors such as CDK4 and Cyclin D1 in the G1 phase, CDK2 and Cyclin A2 in the S phase, and CDK1 and Cyclin B1 in the G2/M phase are highly correlated with advanced stages in bladder carcinoma patients. Altogether, our findings suggest that phytochemical-derived zingerone NPs can be a potent adjuvant agent to provide beneficial chemopreventive and anti-tumorigenesis strategies for human urothelial carcinoma.	bladder
OTUB1 Promotes Stem-like Properties in Bladder Cancer by Stabilising SLC7A11 and Suppressing Ferroptosis through Deubiquitination.	BACKGROUND: Cancer stem cells (CSCs) contribute to bladder cancer (BCa) progression and treatment resistance. Ferroptosis, an iron-dependent cell death, influences CSC maintenance, but its post-translational regulation remains unclear. This study investigated how the deubiquitinase OTUB1 regulated ferroptosis and CSC-like traits in BCa through interaction with SLC7A11. METHODS: OTUB1 expression was assessed in clinical BCa tissue pairs (tumour vs adjacent normal) collected from patients undergoing surgical resection and in cell lines. Gain- and loss-of-function models were established in BCa cells. Cell viability, stemness capacity and ferroptosis markers were evaluated using Cell Counting Kit-8 (CCK-8) assay, Western blot, sphere formation assay, quantitative real-time polymerase chain reaction (qRT-PCR), immunofluorescence, reactive oxygen species (ROS) detection, enzyme-linked immunosorbent assay (ELISA) and co-immunoprecipitation. RESULTS: OTUB1 was significantly upregulated in BCa cells and tissues relative to normal controls (p < 0.01). OTUB1 overexpression significantly enhanced BCa cell viability, self-renewal capacity and stemness marker expression but reduced ferroptosisassociated indicators (ROS, malondialdehyde (MDA) and ferrous iron (Fe(2+))) (p < 0.01). Conversely, OTUB1 knockdown impaired stem-like traits (p < 0.01) and triggered ferroptosis (p < 0.01). Mechanistically, OTUB1 directly interacted with SLC7A11, decreased its ubiquitination and stabilised its protein expression (p < 0.01). Notably, ectopic SLC7A11 expression rescued the impaired stemness and ferroptosis induction caused by OTUB1 knockdown (p < 0.01). CONCLUSIONS: OTUB1 inhibits ferroptosis and sustains CSC-like features in BCa by deubiquitinating and stabilising SLC7A11. The OTUB1-SLC7A11 axis represents a novel regulatory mechanism of CSC maintenance and may serve as an intervention point in BCa.	bladder
A multifunctional M1-like cell vehicle to intravesically deliver ICG for photodynamic therapy of bladder cancer.	Intravesical drug delivery systems often fail to satisfy the requirement of multifunctionality in one entity, including mucoadhesion, tumor-selective binding and deep tumor-penetration. In this work, we engineered the surface of M1-like macrophages with both tumor-targeted and mucoadhesive ligands (R11) to develop a multifunctional cell vehicle (M1(R11)) for intravesical delivery of ICG. Remarkably, M1(R11) corrected the lysosomal trafficking of ICG, directed it to enter the transcellular pathway and thereby enhance its intra-tumoral penetration. When intravesically applied, the M1(R11)-delivered ICG displayed much improved photodynamic efficacy, ultimately eradicating orthotopic bladder tumors in most cases and achieving complete pathological response.	bladder
Evaluation of inflammatory markers in survival analysis of patients undergoing radical cystectomy using machine learning.	BACKGROUND: We aimed to create a Machine learning (ML) model using patient demographic, clinical and pathological data for prediction of overall survival in patients treated with radical cystectomy (RC). Secondly, we evaluated whether inflammatory markers contributed to this model. METHODS: We conducted a retrospective analysis of the institutional cystectomy database and identified consecutive RC patients. Dataset-1 (DS-1) was analyzed in ML models using 30 original features (including the target feature) encompassing preoperative, intraoperative, and postoperative data of the patients. All derived inflammatory markers were cumulatively added to DS-1 to create DS-2, and to test the specific contribution of inflammatory markers, they were systematically integrated in an ordinary order based on their predictive ability (DS-3). Markers without predictive contribution were excluded from the DS-3 model. In addition, the Shapley Additive Explanations (SHAP) method was used to examine the importance of each clinical feature and inflammatory marker. RESULTS: The median age of the 241 patients was 65 years. The mortality rate was 60.2% (145/241). Two- and five-year overall survival (OS) rates were 54.7% and 37.2%, respectively. According to DS-1, F(1) scores were between 0.72 and 0.78. Random Forests and XGBoost models achieved the highest score of 0.78. DS-2 including all inflammatory markers; however, no significant improvement in F(1) scores was observed (0.73-0.78). In DS-3, firstly adding the systemic inflammatory response index (SIRI) to the original features and then neutrophil/lymphocyte ratio (NLR) and platelet/lymphocyte ratio (PLR), achieved the highest F(1) score (0.80) in the Random Forest model. SHAP analyses showed that Tumor (T) stage, preoperative albumin and presence of lympho-vascular invasion (LVI) contributed most to model predictivity. CONCLUSIONS: ML models derived using demographic/clinical features resulted in a maximum F(1) score of 0.78. However, adding the most predictive inflammatory markers in the sequence SIRI, NLR and PLR to demographic data achieved the highest F(1) score of 0.80. Furthermore, T stage and preoperative albumin were the strongest predictive factors in the ML models.	bladder